PathLex, a single lexicon in the Anatomic Pathology domain
The PathLex project is launched by IHE and HL7 Anatomic Pathology, with the collaboration of other
Anatomic Pathology organizations, including the College of American Pathologists, the French Society of
Pathologists and the SEAP (Spanish Society of Pathology). The purpose and scope of the PathLex project is
very similar to those of the RadLex project in the radiology domain. The Pathlex project has been “designed to
satisfy the needs of Anatomic Pathology information system vendors and users by adopting the best features of
existing terminology systems, while producing new terms to fill critical gaps. Rather than “re-inventing the
wheel”, PathLex unifies and supplements other terminology systems”, such as SNOMED-CT, CIM-O or
various vocablary tables defined by DICOM and HL7.
With the recent advances achieved by IHE and HL7 Anatomic Pathology (APW, ARPH and APSR integration
and content profiles1) and DICOM WG 26 (supplement 122 & 145) standard-based informatics transactions
has been defined to support the basic diagnostic workflow in anatomic pathology departments including
managing whole-slide images and semantically rich structured reports in the diagnostic workflow.
As part of these standardization efforts, a key issue is to guaranty that standard messages and document
structures are semantically consistent within and across standards (HL7 v2.5, HL7 v3, DICOM). It is indeed
crucial to guaranty that the same structured clinical information carried out through different information
systems is attached to the same meaning and uniformly interpreted by both human and machines. Since a
variety of terminologies are currently used in the Anatomic pathology domain, there is a need of a single
lexicon that could serve all of their needs. PathLex is designed to fill this need.
PathLex, an “interface terminology” mapped to “reference terminology”
Standard-based transactions used in IHE integration profiles provide a “model of use” 2. Vocabulary tables
defined as part of the standards messages (HL7 v2.5, DICOM IOD) or document templates (HL7 CDA
templates for AP structured reports) used in the Anatomic Pathology domain contain relatively common
clinical terms designed to improve acceptability of information systems to healthcare providers. The aim of
PathLex is to unify in a single lexicon this vocabulary. PathLex is a so-called “interface terminology” defined
by Rosenbloom et al. as “systematic collections of clinically oriented phrases (i.e., ‘terms’) aggregated to
support clinicians’ entry of patient information directly into computer programs, such as clinical
documentation (i.e., ‘note capture’) systems”3.
Despite their prevalence for electronic data capture, no single standard interface terminology exists for
medicine. In contrast, standards have been identified for reference terminologies such as SNOMED CT, the
emerging global health terminology standard published by IHTSDO, that provides unified meanings for
clinical terms from different languages by assigning them to language-independent concepts. Furthermore,
reference terminologies are typically optimized to support the storage, retrieval, and classification of clinical
data. Mapping interface terminologies (as part of a model of use) to standard reference terminologies (as part
of the model of meaning) rather than identifying one or more interface terminologies to serve as standards is
now a commonly admitted strategy towards semantic interoperability.
PathLex, current status
In order to publish, implement and test (during IHE connectathons) IHE APSR content profile) it was decided
to use PathLex to encode Anatomic Pathology observations and AP ancillary technique observations and their
corresponding value.
The current version of PathLex defined by the IHE Anatomic Pathology domain (PathLex - OID :
1.3.6.1.4.1.19376.1.8.2.1) is published as part of the IHE content profile “Anatomic Pathology Structured
Report” (APSR)4. This content profile provides 22 HL7 CDA (a generic template for APSR, a generic
template for cancer APSR and 20 organ-specific templates for cancer APSR). PathLex derives from the APSR
CDA templates; it consists in 1700 terms or expressions corresponding to the display names of the Anatomic
1
Anatomic Pathology Workflow (APW) is an intra hospital integration profiles covering the ordering and performing of
anatomic pathology examinations. Anatomic Reporting for Public Health (ARPH) is an integration profile for sending
anatomic pathology reports to public health organizations. Anatomic Pathology Structured Report (APSR) is a content
profile for sharing or exchanging structured anatomic pathology reports as CDA documents.
2 Benson T. Principles of Health Interoperability HL7 and SNOMED. Springer Verlag, 2009.
3 Rosenbloom ST, Miller RA, Johnson KB. Interface terminologies: facilitating direct entry of clinical data into electronic
health record systems. J Am Med In-form Assoc. 2006 May-Jun;13(3):277-88. Rosenbloom ST, Brown SH, Froehling D,
Bauer BA, Wahner-Roedler DL, Gregg WM, Elkin PL. Using SNOMED CT to represent two interface terminologies. J
Am Med Inform Assoc. 2009 Jan-Feb;16(1):81-8.
4 Available on the ihe.net web site
PathLex, Draft document – IHE Anatomic Pathology
Pathology observation (n=99) and AP ancillary techniques (n=16) and of their corresponding value sets (in
case of coded observations). Theses value sets are specified in the document “Appendix Value Sets for APSR”.
PathLex is available in English and French and is currently being mapped to concept(s) from reference
terminologies like SNOMED CT, SNOMED International V3.5, ADICAP, CIM-O.
PathLex a lexicon to support collaborative digital Anatomic Pathology for patient care
coordination and research activities
An important pre-requisite to the best implementation of Collaborative Digital Anatomic Pathology for both
patient care coordination and research activities, is to provide the “model of meaning” corresponding to the
data & images that are captured, shared and exchanged. Using a reference terminology such as SNOMED CT
offers promising perspectives in terms of scalable semantic queries that could be performed over distributed
Anatomic Pathology Information Systems (APIS), EHRs or Clinical Data Warehouses storing these structured
reports.
Mapping PathLex to SNOMED CT concepts (i.e providing SNOMED CT for Anatomic Pathology
observations and AP ancillary technique observations and their value sets) is therefore a key issue. For some
observations (e.g histologic type) this process is straightforward, for others (e.g TNM) there is no precoordinated SNOMED CT concepts available to represent the meaning of the TNM terms/expressions.
Other issues with regards to the PathLex content could be:
- To extend PathLex with the coded content available in the other standards (HL7 v2.5 and DICOM
IOD) used in the transactions in IHE integration profiles
- To extend PathLex to other domains (e.g inflammatory domain in nephrology)
- To extend PathLex with vocabularies used in research activities (clinical research, biorepositories,
cytogenetics, etc)
PathLex, as a SNOMED extension
There is a need of collaboration between IHTSDO & IHE and especially with IHE Anatomic Pathology (such
collaboration exists with DICOM, HL7, OpenEHR). As stated by K.Spackman during the IHE-HL7-IHTSDO
Anatomic Pathology joint meeting in Vilnius (July 2010), PathLex could be in the future managed as a
SNOMED CT extension. An extension allows authorized organizations to add locally valid content and subsets
without compromising the main body of SNOMED CT. Extensions may contain Concepts, Relationships,
Subsets, Cross Map Sets. These components have the same structure as core components of SNOMED CT.
Concepts in an extension must be subtype descendants from a core concept.
PathLex, a lexicon managed in collaboration (IHE AP, HL7 AP, DICOM WG26, IHTSDO
(IPALM), w3c)
A working group within IHE Anatomic Pathology and HL7 Anatomic Pathology is in charge of defining the
governance of Pathlex and the process and tools required for its management according to this work plan:
- Defining a planning committee in charge of defining the strategy and the methodology of the process
and the priorities in terms of content
- Establishing formal collaboration with reference terminology centers (IHTSDO (International
Pathology and Laboratory Medicine Special Interest Group (IPaLM SIG), NLM, NCI)
- Defining organ system committees in collaboration with anatomic pathology professional and
standards organizations
- Developing (or selecting an existing) collaborative platform dedicated to the management of PathLex
and the mappings with other terminologies
PathLex, Draft document – IHE Anatomic Pathology